sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.040 Å
X-ray
2001-12-01
| Name: | ADP-ribose pyrophosphatase |
|---|---|
| ID: | ADPP_ECOLI |
| AC: | Q93K97 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 3.6.1.13 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 24 % |
| B | 76 % |
| B-Factor: | 22.789 |
|---|---|
| Number of residues: | 54 |
| Including | |
| Standard Amino Acids: | 47 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.428 | 1042.875 |
| % Hydrophobic | % Polar |
|---|---|
| 35.92 | 64.08 |
| According to VolSite | |
| HET Code: | ADV |
|---|---|
| Formula: | C16H23N5O13P2 |
| Molecular weight: | 555.327 g/mol |
| DrugBank ID: | DB01975 |
| Buried Surface Area: | 68.94 % |
| Polar Surface area: | 307.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 6 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 36.909 | 30.3815 | 8.51528 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| C1' | CZ | PHE- 28 | 3.82 | 0 | Hydrophobic |
| N6 | O | GLU- 52 | 2.96 | 150.11 | H-Bond (Ligand Donor) |
| N1 | N | GLU- 52 | 3.04 | 167.63 | H-Bond (Protein Donor) |
| CR5 | CB | ALA- 59 | 3.96 | 0 | Hydrophobic |
| O1B | CZ | ARG- 79 | 3.54 | 0 | Ionic (Protein Cationic) |
| O2B | CZ | ARG- 79 | 3.86 | 0 | Ionic (Protein Cationic) |
| O1B | NH2 | ARG- 79 | 3.49 | 127.9 | H-Bond (Protein Donor) |
| O1B | NH1 | ARG- 79 | 2.73 | 168.98 | H-Bond (Protein Donor) |
| O2B | NH2 | ARG- 79 | 2.96 | 172.8 | H-Bond (Protein Donor) |
| CR4 | CB | ALA- 96 | 4 | 0 | Hydrophobic |
| CX | CB | MET- 98 | 4.45 | 0 | Hydrophobic |
| O2A | N | MET- 98 | 2.99 | 159.07 | H-Bond (Protein Donor) |
| N6 | O | GLY- 135 | 3.1 | 160.84 | H-Bond (Ligand Donor) |
| OR2 | N | GLY- 135 | 3.08 | 141.81 | H-Bond (Protein Donor) |
| OR3 | OE1 | GLU- 139 | 3.3 | 130.06 | H-Bond (Ligand Donor) |
| OR3 | OE2 | GLU- 139 | 2.89 | 162.25 | H-Bond (Ligand Donor) |
| C4' | CG | GLU- 162 | 4.29 | 0 | Hydrophobic |
| C3' | CB | GLU- 162 | 4.38 | 0 | Hydrophobic |
| O2' | O | GLU- 162 | 2.96 | 144.7 | H-Bond (Ligand Donor) |
| C3' | CG | GLU- 164 | 4.35 | 0 | Hydrophobic |
| O1A | MG | MG- 301 | 2.14 | 0 | Metal Acceptor |
| O2A | MG | MG- 304 | 2.21 | 0 | Metal Acceptor |
| O2B | MG | MG- 310 | 2.13 | 0 | Metal Acceptor |
| O1A | MG | MG- 310 | 2.27 | 0 | Metal Acceptor |
